## Visualizing Cerebellum as a Plotly Mesh3d¶

In [1]:
import plotly
print(plotly.__version__)

2.7.0

In [2]:
import numpy as np


Read data for Cerebellum, defined as a triangulated surface:

In [3]:
vertices=np.loadtxt('cerebellum-v.txt', dtype=np.float32)

print (vertices.shape, faces.shape, faces[0,:])

(45406, 3) (90788, 3) [0 1 2]

In [4]:
x,y,z=vertices.T
I, J, K=faces.T

In [5]:
colorscale=[[0.0, 'rgb(253, 225, 197)'],
[0.1, 'rgb(253, 216, 179)'],
[0.2, 'rgb(253, 207, 161)'],
[0.3, 'rgb(253, 194, 140)'],
[0.4, 'rgb(253, 181, 118)'],
[0.5, 'rgb(253, 167, 97)'],
[0.6, 'rgb(253, 153, 78)'],
[0.7, 'rgb(252, 140, 59)'],
[0.8, 'rgb(248, 126, 43)'],
[0.9, 'rgb(243, 112, 27)'],
[1.0, 'rgb(236, 98, 15)']]

In [6]:
mesh=dict(type='mesh3d',
x=x,
y=y,
z=z,
colorscale=colorscale,
intensity= z,
i=I,
j=J,
k=K,
name='',
showscale=False,
lighting=dict(ambient=0.18,
diffuse=1,
fresnel=0.1,
specular=1,
roughness=0.05,
facenormalsepsilon=1e-8,
vertexnormalsepsilon=1e-15),
lightposition=dict(x=100,
y=200,
z=0)
)


In [7]:
axis_style = dict(showbackground=True,
backgroundcolor="rgb(230, 230,230)",
gridcolor="rgb(255, 255, 255)",
zerolinecolor="rgb(255, 255, 255)")
layout=dict(title='Cerebellum',
width=700,
height=700,
font=dict(family='Balto'),
scene=dict(camera=dict(eye=dict( x= 1.15, y=-1.15, z=0.9)),
aspectratio=dict(x=0.85, y=1., z=0.8),
xaxis=dict(axis_style),
yaxis=dict(axis_style),
zaxis=dict(axis_style)
)
)

In [8]:
fig=dict(data=[mesh], layout=layout)

In [ ]:
import plotly.plotly as py
py.sign_in('empet', 'api_key')
py.plot(fig, filename='Cerebellum')


'https://plot.ly/~empet/14286'

In [10]:
from IPython.display import HTML
HTML('<iframe src=https://plot.ly/~empet/14286 width=800 height=800></iframe>')

Out[10]:
In [9]:
from IPython.core.display import HTML
def  css_styling():
return HTML(styles)
css_styling()

Out[9]: